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Top Articles

1Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2Genome Biology201458,325
2Differential expression analysis for sequence count dataGenome Biology201013,707
3DAVID: Database for Annotation, Visualization, and Integrated DiscoveryGenome Biology20037,168
4The Ensembl Variant Effect PredictorGenome Biology20165,181
5DAVID: Database for Annotation, Visualization, and Integrated DiscoveryGenome Biology20034,682
6SCANPY: large-scale single-cell gene expression data analysisGenome Biology20183,958
7OrthoFinder: phylogenetic orthology inference for comparative genomicsGenome Biology20193,367
8Improved metagenomic analysis with Kraken 2Genome Biology20192,909
9OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracyGenome Biology20152,812
10xCell: digitally portraying the tissue cellular heterogeneity landscapeGenome Biology20172,572
11GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancersGenome Biology20112,546
12Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regressionGenome Biology20192,460
13Mash: fast genome and metagenome distance estimation using MinHashGenome Biology20162,099
14MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing dataGenome Biology20152,047
15Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expressionGenome Biology20161,980
16Performance of neural network basecalling tools for Oxford Nanopore sequencingGenome Biology20191,971
17A survey of best practices for RNA-seq data analysisGenome Biology20161,898
18Comprehensive analyses of tumor immunity: implications for cancer immunotherapyGenome Biology20161,768
19Identifying biological themes within lists of genes with EASEGenome Biology20031,664
20HiC-Pro: an optimized and flexible pipeline for Hi-C data processingGenome Biology20151,632
21MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screensGenome Biology20141,614
22GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomesGenome Biology20201,538
23Opportunities and challenges in long-read sequencing data analysisGenome Biology20201,536
24Multi-omics approaches to diseaseGenome Biology20171,439
25The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomesGenome Biology20141,428
26DAVID: Database for Annotation, Visualization, and Integrated DiscoveryGenome Biology20031,411
27Expanded identification and characterization of mammalian circular RNAsGenome Biology20141,361
28Ancient DNA and the rewriting of human history: be sparing with Occam’s razorGenome Biology20161,335
29Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPORGenome Biology20161,334
30BioGPS: an extensible and customizable portal for querying and organizing gene annotation resourcesGenome Biology20091,216
31De novo assembly of bacterial transcriptomes from RNA-seq dataGenome Biology20151,215
32RNA virus interference via CRISPR/Cas13a system in plantsGenome Biology20181,148
33The plant microbiomeGenome Biology20131,028
34Chloroplast genomes: diversity, evolution, and applications in genetic engineeringGenome Biology20161,013
35The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics communityGenome Biology2016985
36Merqury: reference-free quality, completeness, and phasing assessment for genome assembliesGenome Biology2020975
37HiGlass: web-based visual exploration and analysis of genome interaction mapsGenome Biology2018950
38The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screensGenome Biology2019938
39DNA methylation age of blood predicts all-cause mortality in later lifeGenome Biology2015928
40CIRI: an efficient and unbiased algorithm for de novo circular RNA identificationGenome Biology2015921
41deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolutionGenome Biology2016917
42Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profilingGenome Biology2016912
43Pooling across cells to normalize single-cell RNA sequencing data with many zero countsGenome Biology2016912
44PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cellsGenome Biology2019911
45Circlator: automated circularization of genome assemblies using long sequencing readsGenome Biology2015910
46CEL-Seq2: sensitive highly-multiplexed single-cell RNA-SeqGenome Biology2016900
47Transcriptome assembly from long-read RNA-seq alignments with StringTie2Genome Biology2019897
48Cytoscape Automation: empowering workflow-based network analysisGenome Biology2019888
49Ten things you should know about transposable elementsGenome Biology2018817
50The multidimensional mechanisms of long noncoding RNA functionGenome Biology2017802